protected VariantContextWriter createVariantContextWriter(Configuration conf, OutputStream out) { return new VariantContextWriterBuilder().clearOptions() .setOutputStream(out).build(); }
protected VariantContextWriter createVariantContextWriter(Configuration conf, OutputStream out) { return new VariantContextWriterBuilder().clearOptions() .setOutputStream(out).build(); }
@Test(expectedExceptions = IllegalArgumentException.class) public void testUnsupportedDefaultIndexOnTheFlyForStreaming() { new VariantContextWriterBuilder() .setReferenceDictionary(dictionary) .setOutputStream(new ByteArrayOutputStream()) .build(); }
.setOutputStream(outputStream) .setReferenceDictionary(sequenceDictionary) .unsetOption(Options.INDEX_ON_THE_FLY);
@Test(expectedExceptions = IllegalArgumentException.class) public void testInvalidSetFileTypeForStream() { new VariantContextWriterBuilder() .setReferenceDictionary(dictionary) .setOutputStream(new ByteArrayOutputStream()) .setOutputFileType(VariantContextWriterBuilder.OutputType.VCF) .build(); }
private void init( OutputStream output, VCFHeader header, boolean writeHeader) throws IOException { final StoppableOutputStream stopOut = new StoppableOutputStream(!writeHeader, output); writer = new VariantContextWriterBuilder().clearOptions() .setOutputStream(stopOut).build(); writer.writeHeader(header); stopOut.stopped = false; setInputHeader(header); }
@Test(expectedExceptions = IllegalArgumentException.class) public void testUnsupportedIndexOnTheFlyForStreaming() { new VariantContextWriterBuilder() .setReferenceDictionary(dictionary) .setOutputStream(new ByteArrayOutputStream()) .setOption(Options.INDEX_ON_THE_FLY) .build(); }
/** * Create a VariantContextWriter. * * @param outputStream Output stream to write. * @param sequenceDictionary SAM sequence directory (it can be got from VCFHeader) * @param options Writer options * @return The variant context writer */ public static VariantContextWriter createVariantContextWriter(OutputStream outputStream, SAMSequenceDictionary sequenceDictionary, Options ...options) { // setup writer VariantContextWriterBuilder builder = new VariantContextWriterBuilder() .setOutputStream(outputStream) .setReferenceDictionary(sequenceDictionary) .setOption(Options.WRITE_FULL_FORMAT_FIELD) .unsetOption(Options.INDEX_ON_THE_FLY); // options if (options != null) { for (Options option : options) { builder.setOption(option); } } return builder.build(); }
/** * Return a new {@link VariantContextWriter} that uses the header from <code>reader</code> but has the header * extended header through {@link #extendHeaderFields}. * * @param header * the VCF header to use for the construction * @param outStream * {@link OutputStream} to write to * @param additionalHeaderLines * additional {@link VCFHeaderLine}s to add * @return A correct writer for variantContexts */ public static VariantContextWriter openVariantContextWriter(VCFHeader header, OutputStream outStream, Collection<VCFHeaderLine> additionalHeaderLines) { VariantContextWriterBuilder builder = makeBuilder(header); builder.unsetOption(Options.INDEX_ON_THE_FLY); builder.setOutputStream(outStream); // construct VariantContextWriter and write out header VariantContextWriter out = builder.build(); final VCFHeader updatedHeader = extendHeaderFields(new VCFHeader(header)); for (VCFHeaderLine headerLine : additionalHeaderLines) updatedHeader.addMetaDataLine(headerLine); out.writeHeader(updatedHeader); return out; }
@Test public void testSetOutputStream() { final OutputStream stream = new ByteArrayOutputStream(); final VariantContextWriterBuilder builder = new VariantContextWriterBuilder() .setReferenceDictionary(dictionary) .unsetOption(Options.INDEX_ON_THE_FLY) .setOutputStream(stream); VariantContextWriter writer = builder.build(); Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputStream default"); writer = builder.setOption(Options.FORCE_BCF).build(); Assert.assertTrue(writer instanceof BCF2Writer, "testSetOutputStream FORCE_BCF set -> expected BCF stream, was VCF stream"); // test that FORCE_BCF remains in effect, overriding the explicit setting of VCF writer = builder.setOutputVCFStream(stream).build(); Assert.assertTrue(writer instanceof BCF2Writer, "testSetOutputStream FORCE_BCF set 2 -> expected BCF stream, was VCF stream"); writer = builder.unsetOption(Options.FORCE_BCF).build(); Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputStream FORCE_BCF unset -> expected VCF stream, was BCF stream"); writer = builder.setOutputBCFStream(stream).build(); Assert.assertTrue(writer instanceof BCF2Writer, "testSetOutputStream BCF"); writer = builder.setOutputVCFStream(stream).build(); Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputStream VCF"); }
builder.setOutputStream(new FileOutputStream(OUTPUT)); } catch (final FileNotFoundException ex ) { throw new PicardException("Could not open " + OUTPUT.getAbsolutePath() + ": " + ex.getMessage(), ex);
builder.setOutputStream(new FileOutputStream(OUTPUT)); } catch (final FileNotFoundException ex ) { throw new PicardException("Could not open " + OUTPUT.getAbsolutePath() + ": " + ex.getMessage(), ex);